Pyrene and bis-pyrene DNA nucleobase conjugates: excimer and monomer fluorescence of linear and dendronized cytosine and 7-deazaguanine click adducts

Branched and nonbranched nucleoside pyrene click conjugates were prepared from 5-alkynyl-2′-deoxycytidines using pyrene azide in a copper(I)-catalyzed click reaction. Click chemistry was also applied to oligonucleotides to generate pyrene labeled conjugates with linear or dendronized side chains. While dendronized nucleosides carrying two proximal pyrenes show strong excimer fluorescence, single-stranded oligonucleotides containing two pyrene residues attached to a branched chain display only weak or no excimer emission. Contrary, excimer fluorescence was observed for single-stranded oligonucleotides when proximal alkynylated nucleosides were functionalized. Strong excimer fluorescence was also detected for the ‘dC–dG’ base pair modified on both nucleobases with pyrene residues, thus having the fluorescent dye in complementary strands. In general, pyrene fluorescence is strongly quenched by the 7-deazaguanine base (charge transfer), while emission of cytosine linked pyrene is not affected. Pyrene interactions were also demonstrated by Tm increase of DNA duplexes and molecular dynamics simulation.